I always thought the loud click came from the disks parking their heads
before spinning down.

Anyway, it can take several seconds before a disk responds to commands
after having spun down. Often the bus/drive must be reset and the commands
reissued several times before the disk responds. While this isn't a big
problem when running a filesystem or lvm directly on the disks I suspect
this would result in the raid5 module marking the disk as dead.

Can you stop the disks from spinning down using hdparm or similar?

If not, maybe you can access the disks frequently to prevent them from
spinning down. You'll probably have to access them individually, since not
all disks are used when reading/writing a small amount of data.

I want to create a RAID5 array of these drives. Unfortunately after a
varying amount of time of moderate use (though never more than 24 hours)
one of the drives not connected to the 6300ESB just out of the blue
shuts itself down, eventually followed by another at which point the
array is dead.
When the drive shuts down I can hear the familiar click from the drive
cutting its power, and after a bit the following gets logged:

Usually a 'click' just means that the drive is recalibrating because
it has failed to read a sector/track.
You are sure that it's shutting down?

ata9: commant timeout

Ugly.
Does the drive's SMART log say anything interesting?

when using the Promise controllers. The machine locks hard at this
point. With the SuperMicro card the machine remains usable, but the
drives are never to be heared from again.

Bug?
Report it to the Promise maintainer?

The following is logged:
ata14: no device found (phy stat 00000000)
sd 13:0:0:0: SCSI error: return code = 0x40000
end_request: I/O errorm dev sdi, sector 390716676
raid5: Disk failure on sdi2, disabling device.
Pretty much every time it's a different disk,
and I'm unable to revive that disk without a reboot.

Have you tried poking the IDE driver to reset the bus, might get it
running again?
Not a very pretty solution, especially since you might still suffer
two drives going down at once from time to time. Maybe you can patch
MD to pause the array and poke the IDE driver whenever a disk is lost?
Then you would at least only have intermittent failures / timeouts on
a rare basis rather than a non-redundant array when something happens.

I brought this issue to the attention of some WD support people who're
basically telling me that the RAID software is impatient.

If the disk never comes up, being patient surely won't help.
Wait for an hour and see if the drive comes up, ask the WD folks
exactly how patient they want you to be? :-)

When I mount the drives as separate partitions I can play with them to
my heart's content. As a test I filled up 5 drives, copied the data to
the other 5 drives (I'm using the 11th drive, a PATA one, for Linux
itself ATM) and vice versa. As I'm writing this I'm running Bonnie++ in
parallel on these partitions and so far everything's solid as a rock.

Bizarre!...
An idea that will take some amount of work, don't know if it's feasible:
Patch the IDE driver to log everything it does in a ring buffer in memory.
When a drive is lost, dump the buffer contents to disk so you can see
what happened, perhaps even try and reproduce it.
Perhaps the WD folks could even take a look at it..

To the best of my ability I've ruled out hardware faults. The only
thing I can think of now is that the RAID5 module, for whatever reason,
is _telling_ the drive to shutdown, but I can't imagine that happening
without some serious logging going on.